Chemical coating of microwell for electrochemical detection device

ABSTRACT

The described embodiments may provide a method of fabricating a chemical detection device. The method may comprise forming a microwell above a CMOS device. The microwell may comprise a bottom surface and sidewalls. The method may further comprise applying a first chemical to be selectively attached to the bottom surface of the microwell, forming a metal oxide layer on the sidewalls of the microwell, and applying a second chemical to be selectively attached to the sidewalls of the microwell. The second chemical may lack an affinity to the first chemical.

RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.15/194,321, filed Jun. 27, 2016, which is a divisional of U.S. patentapplication Ser. No. 14/139,647 filed Dec. 23, 2013, which is acontinuation of U.S. patent application Ser. No. 13/648,663 filed Oct.10, 2012, which is a continuation of U.S. patent application Ser. No.13/212,685, which claims the benefit of priority to previously filedU.S. provisional patent application Ser. No. 61/374,676 filed Aug. 18,2010, and incorporates the disclosures by reference in their entirety.

This application also incorporates by reference in its entirety the U.S.patent application Ser. No. 12/785,716 filed May 24, 2010.

BACKGROUND

Electrochemical detection is attractive because it provides highsensitivity, small dimensions, low cost, fast response, andcompatibility with microfabrication technologies. (See, e.g., Hughes etal., Science, 254: 74-80 (1991); Mir et al., Electrophoresis, 30:3386-3397 (2009); Trojanowicz, Anal. Chim. Acta, 653: 36-58 (2009); and,Xu et al., Talanta, 80: 8-18 (2009).) These characteristics have led tothe development of a variety of sensors based on amperometric,potentiometric or impedimetric signals and their assembly into arraysfor chemical, biochemical and cellular applications. (See, e.g., Yeow etal., Sensors and Actuators B 44: 434-440 (1997); Martinoia et al.,Biosensors & Bioelectronics, 16: 1043-1050 (2001); Hammond et al., IEEESensors J., 4: 706-712 (2004); Milgrew et al., Sensors and Actuators B103: 37-42 (2004); Milgrew et al., Sensors and Actuators B, 111-112:347-353 (2005); Hizawa et al., Sensors and Actuators B, 117: 509-515(2006); Heer et al., Biosensors and Bioelectronics, 22: 2546-2553(2007); Barbaro et al., Sensors and Actuators B, 118: 41-46 (2006);Anderson et al., Sensors and Actuators B, 129: 79-86 (2008); Rothberg etal., U.S. patent publication 2009/0127589; and, Rothberg et al., U.K.patent application GB24611127.) Typically in such systems, analytes arerandomly distributed among an array of confinement regions, such asmicrowells (also referred to herein as “wells”) or reaction chambers,and reagents are delivered to such regions by a fluidics system thatdirects flows of reagents through a flow cell containing the sensorarray. Microwells in which reactions take place, as well as empty wellswhere no reactions take place, may be monitored by one or moreelectronic sensors associated with each of the microwells.

In one type of electrochemical detection, the fundamental reactionproduct, or “signal”, is a pH change. The pH change is detected bymeasuring a change in the surface charge at the bottom of the well. Thesurface at the bottom of the well buffers the pH change produced as aresult of the biological reaction. The resulting change in surfacecharge due to the biological reaction is sensed by capacitive couplingof the bottom of the well to a floating gate of a chemically-sensitivefield effect transistor (chemFET) below the surface. However, thesidewalls of the well are too far removed from the chemFET to contributeto the chemFET signal. Unfortunately, in current implementations, thesidewalls of the well buffer as well as surface at the bottom of thewell. For example, FIG. 2A shows a prior art microwell structure withnative metal oxide, nitride, or oxinitride surface on both the bottomand sidewall. Hence the sidewall's buffering reduces the signal detectedat the bottom of the well.

In view of the above, it would be advantageous to have available amicrowell structure and a method of conformal coating and selectiveetching of microwell sidewalls that reduce sidewall buffering, whichovercome the deficiencies of current approaches.

BRIEF DESCRIPTION OF THE DRAWING FIGURES

FIG. 1 illustrates a cross-sectional view of a flow cell according to anembodiment of the present teachings.

FIG. 2A illustrates a well structure of the prior art with a nativemetal oxide surface.

FIG. 2B illustrates a well structure with a conformal silanized surfaceaccording to an embodiment of the present teachings.

FIG. 2C illustrates a well structure with a conformal silanized surface,and all horizontal surfaces etched to the original metal oxide accordingto an embodiment of the present teachings.

FIG. 3A illustrates the molecular structure of a PEG-Silane of one typeof silane that can be used for the conformal coating process of themicrowells according to an embodiment of the present teachings.

FIG. 3B illustrates the molecular structure of another type of silanethat can be used for the conformal coating process of the microwellaccording to an embodiment of the present teachings.

FIG. 3C illustrates the molecular structure of a zwitter ionic speciessilane that can be used for the conformal coating process of themicrowells according to an embodiment of the present teachings.

FIGS. 4A-4C illustrate different stages of fabricating a well structureaccording to an embodiment of the present teachings.

FIG. 5 illustrates a process of fabricating a well structure of FIG. 4Caccording to an embodiment of the present teachings.

FIGS. 6A-6F illustrate different stages of fabricating another wellstructure according to an embodiment of the present teachings.

FIG. 7 illustrates a process of fabricating a well structure of FIG. 6Faccording to an embodiment of the present teachings.

FIG. 8 illustrates a well structure according to another embodiment ofthe present teachings.

FIGS. 9A-9E illustrate different stages of fabricating a well structureaccording to another embodiment of the present teachings.

FIG. 10 illustrates a process of fabricating a well structure of FIG. 9Eaccording to an embodiment of the present teachings.

FIG. 11 illustrates a chemical sensing process according to anembodiment of the present teachings.

DETAILED DESCRIPTION

The described embodiments may provide a chemical detection device withan improved signal-to-noise ratio (SNR). The chemical detection devicemay include a microwell coated with a chemical that binds to the bottomof the microwell and facilitates binding of an ion and a CMOS deviceplaced underneath the bottom of the microwell. In different embodiments,the sidewalls of the microwell may be made of silicon dioxide (SiO₂) orplastic. In one embodiment, the sidewalls of the microwell may be coatedwith a silane group that reduces buffering of protons in solutions. TheSNR may be improved by a reduction of buffering of protons by thesidewalls.

One embodiment may provide a method of fabricating a chemical detectiondevice with an improved signal-to-noise ratio. The method may compriseforming a plastic layer on top of a CMOS device, forming a layer ofmetal oxide on top of the plastic layer, forming a microwell on theplastic layer on top of the CMOS device by anisotropic plastic etching,and applying a chemical that binds to the bottom of the microwell butdoes not bind to the plastic sidewall.

Another embodiment may provide a method of fabricating a chemicaldetection device with an improved signal-to-noise ratio. The method maycomprise forming an opening of a microwell on a metal oxide layer on topof a silicon dioxide (SiO₂) layer. The SiO₂ layer may be on top of aCMOS device. The method may further comprise forming a circular undercuton the SiO₂ layer underneath an edge of the opening of the microwell,forming the microwell on the SiO₂ layer on top of the CMOS device byanisotropic SiO₂ etching, applying one chemical that binds to thesidewalls and at the bottom of the microwell, deactivating the chemicalat the bottom of the microwell, and applying another chemical thatlocates at the bottom of the microwell and facilitates binding of ions.

A further embodiment may provide a method of fabricating a chemicaldetection device with an improved signal-to-noise ratio. The method maycomprise forming a metal oxide layer on top of a silicon dioxide (SiO₂)layer. The SiO₂ layer may be on top of a CMOS device. The method mayfurther comprise forming a microwell on the SiO₂ layer on top of theCMOS device, applying a chemical that binds to a sidewall and a bottomof the microwell, and etching away the chemical at the bottom of themicrowell.

Another embodiment may provide a method of fabricating a chemicaldetection device with an improved signal-to-noise ratio. The method maycomprise forming a microwell in a silicon dioxide (SiO₂) layer on top ofa CMOS device, applying a chemical to be selectively attached to thebottom of the microwell, forming a metal oxide layer on the top edgesand sidewalls of the microwell, and applying another chemical to beselectively attached to the top edges and sidewalls of the microwell.

FIG. 1 is an expanded and cross-sectional view of flow cell 100 showinga portion of a flow chamber 106 with reagent flow 108 moving across thesurface of microwell array 102 over the open ends of the microwells.Microwell array 102 and sensor array 105 together may form an integratedunit forming a bottom wall or floor of flow cell 100. In one embodiment,reference electrode 104 may be fluidly connected to flow chamber 106. Amicrowell 101 and sensor 114 are shown in an expanded view. Microwell101 may be formed in the bulk material 110 by any conventionalmicrofabrication technique. The volume, shape, aspect ratio (such asbase width-to-well depth ratio), and other dimensional characteristicsof the microwells may be design choices that depend on a particularapplication, including the nature of the reaction taking place, as wellas the reagents, byproducts, and labeling techniques (if any) that areemployed. The sensor 114 may be a chemFET with a floating gate 118having a sensor plate 120 separated from the microwell interior by apassivation layer 116. The sensor 114 may be predominantly responsive to(and generates an output signal related to) the amount of charge 124present on the passivation layer 116 opposite of the sensor plate 120.Changes in charge 124 may cause changes in the current between source121 and drain 122 of the FET, which may be used directly to provide acurrent-based output signal or indirectly with additional circuitry toprovide a voltage-based output signal. Reactants, wash solutions, andother reagents may move into microwells from flow chamber 106 primarilyby diffusion 140.

In one embodiment, reactions carried out in microwell 101 may beanalytical reactions to identify or determine characteristics orproperties of an analyte of interest. Such reactions may generatedirectly or indirectly byproducts that affect the amount of chargeadjacent the sensor plate 120. (Indirect detection may occur, forexample, if byproduct chelators or other binding compounds are used thataffect the sensor after binding an analyte of interest or if labelingmoieties are employed, such as enzymes that may generate a secondarybyproduct as the result of a binding event, or the like). If suchbyproducts are produced in small amounts or rapidly decay or react withother constituents, then multiple copies of the same analyte may beanalyzed in microwell 101 at the same time in order to increase theoutput signal ultimately generated. In one embodiment, multiple copiesof an analyte may be attached to a solid phase support 112, eitherbefore or after deposition into a microwell. The solid phase support 112may be microparticles, nanoparticles, beads, solid and porous comprisinggels, and the like. For nucleic acid analyte, multiple, connected copiesmay be made by rolling circle amplification (RCA), exponential RCA, andlike techniques, to produce an amplicon without the need of a solidsupport.

In one embodiment, the byproduct produced as a result of genomic DNAfragment sequencing is a pH change due to the incorporation of anucleotide. In an embodiment, this may occur at an appropriate operatingpH of between 7.5 and 7.8. Approximately one proton is released pernucleotide that is incorporated under the given conditions. The pHchange is detected by measuring the change in the charge of the surfaceon the bottom of the well. The surface on the bottom and the sides of awell are typically composed of a metal oxide or nitride. The surface maycomprise a number of surface groups that undergo charging reactions.These charging reactions can be described using the equations below:M-OH↔M-O⁻+H⁺  (1)M-OH+H⁺↔M-OH₂ ⁺  (2)

The number of surface groups, along with the characteristic equilibriumconstants associated with the charging reactions above, impart abuffering capacity to the surface. The surface buffering capacity in alimited sample volume, such as a microwell, will buffer the pH changeassociated with the biological incorporation reaction. The change insurface charge due to the charging reactions (equations (1) and (2)above) may be sensed by capacitively coupling the bottom of the well toa chemFET located below the bottom surface of the well. As discussed inthe Background section, however, the sidewalls of the well are too farremoved from the chemFET to contribute to the chemFET signal. Therefore,embodiments of the present invention use conformal coating todifferentiate the sidewalls and the bottom of the well, and thus reducethe sidewall buffering.

FIGS. 2B and 2C show one embodiment of the present invention whichsolves the problem of sidewall buffering by conformal coating of thenative metal oxide, nitride, or oxinitride surface layer, followed byselective etching of all horizontal surfaces. FIG. 2B shows theconformal coating of all surfaces of the microwell with silane, inaccordance with one embodiment of the present invention. As shown inFIG. 2B, microwells 202 may be covered (both on the bottom andsidewalls) by a layer 204. The layer 204, for example, may be a layer ofchemical that lacks an affinity for protons. The conformal coatingreduces or eliminates surface groups that can undergo reactions withprotons in solution and hence reduces or eliminates the bufferingcapacity of said surfaces. For example, when the layer 204 is removedfrom the bottom of the microwells 202, the layer 204 on the sidewallsmay help reduce or eliminate buffering capacity of the sidewalls of themicrowells. FIG. 2C shows the results of the selective etching ofhorizontal surfaces only (including the bottom of the wells and topedges between wells), restoring the native metal oxide, nitride, oroxinitride surface, and hence allows the pH sensing to occur selectivelyat the bottom of the well. Different techniques for etching thehorizontal surfaces can be employed. In an embodiment, the etching isaccomplished using a directional reactive ion etch of the horizontalsurfaces (e.g., Bosch process).

FIGS. 3A-3C shows different types of silane that can be used for theconformal coating process. FIG. 3A shows the structure of PEG-Silanethat can be used in the conformal coating process. It may be availablefrom NANOCS.com (Product code PEG6-0 I 02) and has an average MW ofPEG=2000. It may impart a hydrophilic surface that does not change incharge with small changes in pH around the operating pH (e.g., pH rangeof 7.5 to 7.8). FIG. 3B shows the structure ofN,N,N-trimethyl-3-(trimethoxysilyl)-I-propanaminium chloride silane thatcan be used in the conformal coating process. It may be available fromSigma Aldrich (Product #595888). It may impart a hydrophilic positivecharge to all vertical surfaces. The charge on the surface does notrespond to small changes in pH around the operating pH. FIG. 3C showsthe structure of a zwitter ionic species silane that can be used in theconformal coating process. It is available in a single step reactionusing propane sultone and APTMS. It may impart a highly hydrophilic butoverall neutral coating to the sidewalls.

FIGS. 4A-4C illustrate cross-sectional views of different stages offabricating a well structure according to an embodiment of the presentteachings. FIG. 4A shows a cross-sectional view of a part of a chemicalsensing device 400 before microwells are formed. The chemical sensingdevice 400 may comprise a metal oxide layer 402, a microwell layer 404,a CMOS device layer 406 and charge sensitive devices 408.1 and 408.2between the microwell layer 404 and the CMOS device layer 406. The metaloxide layer 402 may be on top of the microwell layer 404, which in turnmay be on top of the CMOS device layer 406. The charge sensitive devices408.1 and 408.2 may each represent a top portion of a chemFET. Forexample, the charge sensitive devices 408.1 and 408.2 may be thepassivation layers of the chemFETs (e.g., passivation layer 116 of FIG.1), while the floating gate structures of the chemFETs may be underneaththe charge sensitive devices 408.1 and 408.2 (not shown). In oneembodiment, the microwell layer 404 may be a layer of plastic (e.g.,Cytop, TEFLON, Parylene, etc.). Further, in one embodiment, the chargesensitive devices 408.1 and 408.2 may each comprise two or more layersof metal oxides. For example, each of the charge sensitive devices 408.1and 408.2 may comprise a top layer of tantalum pentoxide (Ta₂O₅) and abottom layer of aluminum oxide (Al₂O₃). The metal oxide layer 402 maycomprise one or more layers of Ta₂O₅, Hafnium dioxide (HfO₂), zirconiumoxide (ZrO₂), or Al₂O₃. The CMOS device layer may be a layer ofsemiconductor material (e.g., Si).

FIG. 4B shows a cross-sectional view of the chemical sensing device 400with a pair of microwells 410. The microwells 410 may be etched on themetal oxide layer 402 and the microwell layer 404. In one embodiment,the microwells 410 may be etched to expose the top of the chargesensitive devices 408.1 and 408.2. The microwells 410 may be etched, forexample, by anisotropic etching. FIG. 4C shows a cross-sectional view ofthe chemical sensing device 400 after a chemical may be applied to it.The applied chemical, shown as wiggly lines 412, may be coated only atthe bottom of the microwells because of inert property of the plasticsidewall. In one embodiment, the plastic sidewalls may have zerobuffering because of the inert property. In one embodiment, the chemicalmay be phosphate, phosphonate, or silane.

FIG. 5 illustrates a process 500 of fabricating a well structure of FIG.4C according to an embodiment of the present teachings. At block 502,the process 500 may form a layer of plastic on top of a CMOS devicelayer. As shown in FIG. 4A, the plastic layer 404 may be formed on topof the CMOS device layer 406. Then at block 504, the process 500 mayform a layer of metal oxide on top of the plastic layer. For example,the metal oxide layer 402 may be formed on top of the plastic layer 404in FIG. 4A. The process 500 may then proceed to block 506. At block 506,a microwell may be formed on the plastic layer on top of the CMOS devicelayer. As described above with respect to FIG. 4B, the etching on theplastic layer may be performed by anisotropic plastic etching. At block508, a chemical may be applied. The chemical (e.g., the wiggly lines412) may bind only to the bottom of the microwell, for example, becauseof the inert property of the plastic sidewall.

FIGS. 6A-6F illustrate cross-sectional views of different stages offabricating a well structure according to another embodiment of thepresent teachings. FIG. 6A shows a cross-sectional view of a part of achemical sensing device 600 before microwells are formed. The chemicalsensing device 600 may comprise a metal oxide layer 602, a microwelllayer 604, a CMOS device layer 606 and charge sensitive devices 608.1and 608.2 between the microwell layer 604 and the CMOS device layer 606.The metal oxide layer 602 may be on top of the microwell layer 604,which in turn may be on top of the CMOS device layer 606. The chargesensitive devices 608.1 and 608.2 may each represent a top portion of achemFET. For example, the charge sensitive devices 608.1 and 608.2 maybe the passivation layers of the chemFETs (e.g., passivation layer 116of FIG. 1), while the floating gate structures of the chemFETs may beunderneath the charge sensitive devices 608.1 and 608.2 (not shown). Inone embodiment, the microwell layer 604 may be a layer of silicon oxide(SiO₂). Further, in one embodiment, the charge sensitive devices 608.1and 608.2 may each comprise two or more layers of metal oxides. Forexample, each of the charge sensitive devices 608.1 and 608.2 maycomprise a top layer of Ta₂O₅ and a bottom layer of Al₂O₃. The metaloxide layer 602 may comprise one or more layers of Ta₂O₅, HfO₂, ZrO₂, orAl₂O₃. The CMOS device layer 606 may be a layer of semiconductormaterial (e.g., Si).

FIG. 6B shows a cross-sectional view of the chemical sensing device 600with a pair of microwells 610 being formed. The openings of themicrowells 610 may be etched on the metal oxide layer 602 and the upperportion of the microwell layer 604. As shown in FIG. 6B, underneath theopening edges of the metal oxide layer 602, upper portion of themicrowell layer 604 may be etched to create undercuts. In oneembodiment, the undercuts may be created by isotropic SiO₂ etching. FIG.6C shows a cross-sectional view of the chemical sensing device 600 withthe pair of microwells 610 having been formed. In one embodiment, themicrowells 610 may be etched to expose the top of the charge sensitivedevices 608.1 and 608.2. The microwells 610 may be formed by anisotropicSiO₂ etching. FIG. 6D shows a cross-sectional view of the chemicalsensing device 600 after application of a chemical. The appliedchemical, shown as wiggly lines 612, may be coated to cover sidewallsand bottom of the microwells 610. In one embodiment, the chemical may bea silane group.

FIG. 6E shows a cross-sectional view of the chemical sensing device 600with the bottom of the pair of microwells 610 having been cleaned of theapplied chemical. In one embodiment, the microwells 610 may be etched toclean the applied chemical and expose the top of the charge sensitivedevices 608.1 and 608.2. The bottom of the microwells 610 may be cleanedby directional etching, reactive ion etching, sacrificial layer etching,or combination of these etching techniques. If the sacrificial layeretching is used, a sacrificial layer may be created on top of the metaloxide sensing layers of the charge sensitive devices 608.1 and 608.2before the chemical is applied. After the chemical is applied, thesacrificial layer may be etched to strip the chemical at the bottom ofthe microwells 610 to expose the metal oxide sensing layers of thecharge sensitive devices 608.1 and 608.2. In another embodiment, thechemical may be deactivated by other means, such as, for example,covered or chemically rendered inactive.

FIG. 6F shows a cross-sectional view of the chemical sensing device 600after application of another chemical. The other applied chemical, whichmay be referred to as the first chemical and shown as bolded wigglylines 614, may be coated to cover the bottom of the microwells 610. Inone embodiment, the other chemical may be one or more chemicals selectedfrom a group including: phosphate, phosphonate, catechol, nitrocatechol,boronate, phenylboronate, imidazole, silanol or other pH-sensing group.The other chemical may be positively charged to help bead loading andhelp accumulation of electrical charges caused by chemical reactions.

In one embodiment, the other chemical may be absent. That is, thechemical sensing device 600 may have the sidewalls of microwells 610coated with one group of chemicals and may leave the bottom of themicrowells 610 exposed. By coating only the sidewalls with one group ofchemicals, the buffering of electrical charges by the sidewalls may bereduced or eliminated, and the SNR may be improved.

FIG. 7 illustrates a process of fabricating a well structure of FIG. 6Faccording to an embodiment of the present teachings. At block 702, anopening of a microwell may be formed on a metal oxide layer on top of asilicon dioxide (SiO₂) layer and the SiO₂ layer may be on top of a CMOSdevice layer. Then at block 704, a circular undercut may be formed onthe SiO₂ layer underneath an edge of the opening of the microwell. Asshown in FIG. 6B, opening and undercuts around the opening for themicrowells 610 may be formed on the metal oxide layer 602 and microwelllayer 606. As described above with respect to FIG. 6B, the undercuts maybe created by isotropic SiO₂ etching. At block 706, a microwell may beformed on the SiO₂ layer on top of the CMOS device layer. For example,anisotropic SiO₂ etching may be used to etch the microwells. At block708, a chemical may be applied to the microwell. The chemical may bindto the sidewall and bottom of the microwell, and cover the sidewall andbottom of the microwell. At block 710, the chemical at the bottom of themicrowell may be deactivated. For example, the chemical may be removed(e.g., by directional etching, reactive ion etching, sacrificial layeretching, or combination thereof), inactivated by chemicals, or covered.At block 712, another chemical may be applied to the microwell. Theother chemical may bind to the bottom of the microwell and facilitatebinding of ions.

FIG. 8 illustrates a well structure according to another embodiment ofthe present teachings. The well structure of FIG. 8 may comprise a metaloxide layer 802, a microwell layer 804, a CMOS device layer 806 and achemical sensing device 808.1 or 808.2. The metal oxide layer 802 may beon top of the microwell layer 804, which in turn may be on top of theCMOS device layer 806. The charge sensitive devices 808.1 and 808.2 maybe exposed in the microwells 810. The sidewalls and peripheral edges 816of the bottom of the microwells 810 may be covered by a second chemical812 (non-bolded wiggly lines). The peripheral edges 816 may be portionsof the bottom of the microwell 810 around the charge sensitive devices818.1 and 808.2. The top surfaces of the chemical sensing devices 808.1and 808.2 may be covered by a first chemical 814 (bolded wiggly lines).In one embodiment, as shown in FIG. 8, the microwells 810 may each havean inversed tapered shape. That is, the bottom of the microwells 810 mayhave a larger diameter than the top of the microwells 810 and thus, thesidewalls may be inversely inclined. In one embodiment, the metal oxidelayer 802 may comprise one or more layers of Ta₂O₅, HfO₂, ZrO₂, orAl₂O₃; the microwell layer 806 may be a layer of SiO₂; and the CMOSdevice layer 806 may be a layer of semiconductor material (e.g., Si).The microwells 810 may be etched using directional etching, reactive ionetching, sacrificial layer etching, or combination thereof.

FIGS. 9A-9E illustrate cross-sectional views of different stages offabricating a well structure according to another embodiment of thepresent teachings. FIG. 9A shows a cross-sectional view of a part of achemical sensing device 900 before any microwells are formed. Thechemical sensing device 900 may comprise a microwell layer 902 on top ofa CMOS device layer 904, and a charge sensitive device 906 embeddedbetween the microwell layer 902 and CMOS device layer 904. The embeddeddevice 906 may represent a top portion of a chemFET. For example, theembedded device 906 may be the passivation layer of a chemFET (e.g.,passivation layer 116 of FIG. 1), the floating gate structure of thechemFET may be underneath the device 906 (not shown). In one embodiment,the microwell layer 902 may be a layer of SiO₂. Further, in oneembodiment, the device 906 may comprise two or more layers of metaloxides. For example, the device 906 may comprise a top layer of Ta₂O₅and a bottom layer of Al₂O₃. The CMOS device layer may be a layer ofsemiconductor material (e.g., Si).

FIG. 9B shows a cross-sectional view of the chemical sensing device 900with a microwell 908. The microwell 908 may be etched on the microwelllayer 902. In one embodiment, the microwell 908 may be etched to exposethe top of the device 906. The microwells 908 may be etched byanisotropic SiO₂ etching. FIG. 9C shows a cross-sectional view of thechemical sensing device 900 after application of a chemical. The appliedchemical, shown as the bolded wiggly lines 910, may be coated only atthe bottom of the microwell 908 because of chemical properties of thesurface of the charge sensitive device 906. For example, the surface ofthe charge sensitive device 906 may have selective affinity of phosphateor phosphonate, or a silane group. In one embodiment, the chemical maybe a phosphate, phosphonate, catechol, nitrocatechol, boronate,phenylboronate, imidazole, silanol or other pH-sensing group.

FIG. 9D shows a cross-sectional view of the chemical sensing device 900after the sidewalls and top horizontal portions 916 (also referred toherein as “top edge” or “horizontal surface proximate to top edge ofsidewall”) of the microwell 908 is covered by a layer 912 of metaloxide. In one embodiment, the metal oxide layer 912 may be amono-molecular layer. For example, the mono-molecular layer may be ametal oxide formed by a chemo selective reaction of well wall oxide(such as silicon dioxide) with Zirconium alkoxides followed byhydrolysis post reaction. That is, the metal oxide layer 912 may be alayer of a solvent based deposition of ZrO₂. The metal oxide layer 912is not disposed along the bottom portion of the well, as shown in FIG.9D, due to the lack of affinity between the metal oxide layer 912 andthe chemical 910, according to an embodiment of the present teachings.In effect, the chemical 910 may serve as a “mask” or aprotective/barrier layer to prevent the metal oxide layer 912 from beingdisposed along the bottom of the microwell. FIG. 9E shows across-sectional view of the chemical sensing device 900 afterapplication of another chemical. The other chemical, shown as thenon-bolded wiggly lines 914, may be coated at the sidewalls and tophorizontal portions of the microwell 908 because of chemical propertiesof the surface of the metal oxide layer 912. In one embodiment, theother chemical may be a PEG phosphate or phosphonate. To be consistentwith previous embodiments, the chemical coated at the bottom of themicrowell 908 may be referred to as the first chemical and the chemicalcoated at the sidewalls may be referred to as the second chemical.

The neutral PEG surfaces at the sidewalls of the microwell 908 mayreduce, or eliminate, the proton buffering at the sidewalls. Further,the phosphate or phosphonate coated at the bottom of the microwell maygive positive charge to improve bead loading or DNA primers to furtherboost sequencing signal-to-noise ration (SNR).

FIG. 10 illustrates a process 1000 of fabricating a well structure ofFIG. 9E according to an embodiment of the present teachings. At block1002, a microwell may be formed in a silicon dioxide (SiO₂) layer on topof a CMOS device. As shown in FIG. 9B, the microwell 908 may be formedin the SiO₂ layer 902. Then at block 1004, a chemical may be applied tobe selectively attached to the bottom of the microwell. For example, afirst chemical may be applied and selectively attached to the topsurface of the charge sensitive device 906 in the microwell 908. Atblock 1006, a metal oxide layer on the sidewalls and top horizontalportions of the microwell may be formed. As described above with respectto FIG. 9D, a solvent based deposition of ZrO₂ mono-molecular layer maybe created at the sidewalls and top horizontal portions of the microwell908. At block 1008, a second chemical may be applied that selectivelyattaches to the sidewalls and top horizontal portions of the microwell.The second chemical (e.g., the non-bolded wiggly lines 914 of FIG. 9E)may bind only to the metal oxide layer 912 of the microwell at thesidewalls and top horizontal portions, for example, because of thechemical properties of the other chemical and metal oxide layer 912.

In one embodiment, microwells may be made on a layer of metal that isplaced on top of a CMOS device layer. That is, for example, themicrowell layer 902 may be a layer of metal, such as, Al, Cu or Ti. Inthis embodiment, the bottom of the microwells may be coated by the firstchemical, or the sidewalls of the microwells may be coated by the secondchemical, or both. Further, in this embodiment, the top edges of themicrowells may be covered by a metal oxide layer, such as one or morelayers of tantalum pentoxide (Ta₂O₅), aluminum oxide (Al₂O₃), Hafniumdioxide (HfO₂), or zirconium oxide (ZrO₂). The fabrication for metalmicrowells may use Damascene or dual Damascene process. For example, usephotolithography to make negative pillar patterns, deposit a seed layer,perform metal electrical plating, polish the metal and then etch thenegative pillar patterns to form metal microwells. See, e.g., Ohmori, etal., Japanese Journal of Applied Physics 49 05FD01: 1-4 (2010), thecontent of which is incorporated herein by reference.

In one embodiment, the silane group for the second chemical may beR—[(CH2)n]-Si—[X1X2X3] where R is an organofunctional group, [(CH2)n] isa hydrocarbon linker (n=1 to 20) Si is a silicon atom, and [X1X2X3]comprises one or more independent hydrolysable groups, including alkoxyor halogen groups. In another embodiment, the silane group for thesecond chemical may be R—[(C2H4O)n]-Si—[X1X2X3] where R is anorganofunctional group, [(C2H4O)n] (n=1 to 100) is a polyether linker,Si is a silicon atom, and [X1X2X3] comprises one or more hydrolysablegroups, including alkoxy or halogen groups. In either of theembodiments, organofunctional groups R include, but are not limited tomethyl, methylene, phenyl, benzyl, anilino, amino, amide, hydroxyl,aldehyde, alkoxy, halo, mercapto, carboxy, acyl, vinyl, allyl, styryl,epoxy, isocyanato, glycidoxy, and acryloxy.

Examples of the silane group for the second chemical may include:

-   N-(6-AMINOHEXYL)AMINOMETHYLTRIETHOXYSILANE,-   (MERCAPTOMETHYL)METHYLDIETHOXYSILANE,-   CHLOROMETHYLTRIETHOXYSILANE,-   (ISOCYANATOMETHYL)METHYLDIMETHOXYSILANE,-   N-PHENYLAMINOMETHYLTRIETHOXYSILANE,-   TRIETHOXYSILYLUNDECANAL,-   11-MERCAPTOUNDECYLTRIMETHOXYSILANE,-   10-UNDECENYLTRIMETHOXYSILANE,-   N-(2-AMINOETHYL)-11-AMINOUNDECYLTRIMETHOXYSILANE,-   11-BROMOUNDECYLTRIMETHOXYSILANE,-   n-OCTYLTRIETHOXYSILANE,-   2-[METHOXY(POLYETHYLENEOXY)PROPYL]TRIMETHOXYSILANE,-   3-METHOXYPROPYLTRIMETHOXYSILANE,-   METHOXYTRIETHYLENOXYPROPYLTRISILANE,-   METHOXYSILANE,-   METHOXYETHOXYUNDECYLTRICHLOROSILANE,-   2-[METHOXY(POLYETHYLENEOXY)PROPYL]-TRICHLOROSILANE.

FIG. 11 illustrates a chemical sensing process 1100 according to anembodiment of the present teachings. At block 1102, a solid phasesupport with a plurality of analytes attached thereto may be depositedinto a microwell. For example, a plurality of analytes may be attachedto the solid phase support 112 and the solid phase support 112 may bedeposited into the microwell 101. The microwell may have a bottomsurface and sidewalls. In one embodiment, the bottom surface may becovered in a first chemical that facilitates pH sensing and thesidewalls may be covered in a second chemical that reduces buffering ofprotons in the solution. At block 1104, a charge at the bottom surfaceof the microwell may be sensed. As described with respect to equations(1) and (2), the charge may be due to one or more byproducts generatedby at least one chemical reactions with the plurality of analytes. Inone embodiment, the chemical sensing process 1100 may be a DNA sequencesensing process. That is, each of the plurality of analytes may be asample DNA fragment. The DNA sequence may be determined by subsequentlysupplying different reagents to the microwell 101 and detectingbyproducts of chemical reactions.

Several embodiments of the present invention are specificallyillustrated and described herein. However, it will be appreciated thatmodifications and variations of the present invention are covered by theabove teachings. In other instances, well-known operations, componentsand circuits have not been described in detail so as not to obscure theembodiments. It can be appreciated that the specific structural andfunctional details disclosed herein may be representative and do notnecessarily limit the scope of the embodiments. For example, someembodiments are described using CMOS technology. A skilled artisan wouldappreciate that a CMOS device may be used to refer to a pure PMOS deviceor a pure NMOS device, or a combination of PMOS and NMOS devices.

Those skilled in the art may appreciate from the foregoing descriptionthat the present invention may be implemented in a variety of forms, andthat the various embodiments may be implemented alone or in combination.Therefore, while the embodiments of the present invention have beendescribed in connection with particular examples thereof, the true scopeof the embodiments and/or methods of the present invention should not beso limited since other modifications will become apparent to the skilledpractitioner upon a study of the drawings, specification, and followingclaims.

Various embodiments may be implemented using hardware elements, softwareelements, or a combination of both. Examples of hardware elements mayinclude processors, microprocessors, circuits, circuit elements (e.g.,transistors, resistors, capacitors, inductors, and so forth), integratedcircuits, application specific integrated circuits (ASIC), programmablelogic devices (PLD), digital signal processors (DSP), field programmablegate array (FPGA), logic gates, registers, semiconductor device, chips,microchips, chip sets, and so forth. Examples of software may includesoftware components, programs, applications, computer programs,application programs, system programs, machine programs, operatingsystem software, middleware, firmware, software modules, routines,subroutines, functions, methods, procedures, software interfaces,application program interfaces (API), instruction sets, computing code,computer code, code segments, computer code segments, words, values,symbols, or any combination thereof. Determining whether an embodimentis implemented using hardware elements and/or software elements may varyin accordance with any number of factors, such as desired computationalrate, power levels, heat tolerances, processing cycle budget, input datarates, output data rates, memory resources, data bus speeds and otherdesign or performance constraints.

Some embodiments may be implemented, for example, using acomputer-readable medium or article which may store an instruction or aset of instructions that, if executed by a machine, may cause themachine to perform a method and/or operations in accordance with theembodiments. Such a machine may include, for example, any suitableprocessing platform, computing platform, computing device, processingdevice, computing system, processing system, computer, processor, or thelike, and may be implemented using any suitable combination of hardwareand/or software. The computer-readable medium or article may include,for example, any suitable type of memory unit, memory device, memoryarticle, memory medium, storage device, storage article, storage mediumand/or storage unit, for example, memory, removable or non-removablemedia, erasable or non-erasable media, writeable or re-writeable media,digital or analog media, hard disk, floppy disk, Compact Disc Read OnlyMemory (CD-ROM), Compact Disc Recordable (CD-R), Compact DiscRewriteable (CD-RW), optical disk, magnetic media, magneto-opticalmedia, removable memory cards or disks, various types of DigitalVersatile Disc (DVD), a tape, a cassette, or the like. The instructionsmay include any suitable type of code, such as source code, compiledcode, interpreted code, executable code, static code, dynamic code,encrypted code, and the like, implemented using any suitable high-level,low-level, object-oriented, visual, compiled and/or interpretedprogramming language.

“Amplicon” means the product of a polynucleotide amplification reaction.That is, a clonal population of polynucleotides, which may be singlestranded or double stranded, which are replicated from one or morestarting sequences. The one or more starting sequences may be one ormore copies of the same sequence, or they may be a mixture of differentsequences that contain a common region that is amplified, for example, aspecific exon sequence present in a mixture of DNA fragments extractedfrom a sample. Amplicons are formed by the amplification of a singlestarting sequence. Amplicons may be produced by a variety ofamplification reactions whose products comprise replicates of the one ormore starting, or target, nucleic acids. In one aspect, amplificationreactions producing amplicons are “template-driven” in that base pairingof reactants, either nucleotides or oligonucleotides, have complementsin a template polynucleotide that are required for the creation ofreaction products. In one aspect, template-driven reactions are primerextensions with a nucleic acid polymerase or oligonucleotide ligationswith a nucleic acid ligase. Such reactions include, but are not limitedto, polymerase chain reactions (PCRs), linear polymerase reactions,nucleic acid sequence-based amplification (NASBAs), rolling circleamplifications, and the like, disclosed in the following references thatare incorporated herein by reference: Mullis et al., U.S. Pat. Nos.4,683,195, 4,965,188, 4,683,202, and 4,800,159 (PCR); Gelfand et al.,U.S. Pat. No. 5,210,015 (real-time PCR with “taqman” probes); Wittwer etal., U.S. Pat. No. 6,174,670; Kacian et al., U.S. Pat. No. 5,399,491(“NASBA”); Lizardi, U.S. Pat. No. 5,854,033; Aono et al., Japanesepatent publ. JP 4-262799 (rolling circle amplification); and the like.In one aspect, amplicons are produced by PCRs. As used herein, the term“amplifying” means performing an amplification reaction. A “reactionmixture” means a solution containing all the necessary reactants forperforming a reaction, which may include, but not be limited to,buffering agents to maintain pH at a selected level during a reaction,salts, co-factors, scavengers, and the like. A “solid phase amplicon”means a solid phase support, such as a particle or bead, having attacheda clonal population of nucleic acid sequences, which may have beenproduced by a process such as emulsion PCR, or like technique.

“Analyte” means a molecule or biological cell of interest that directlyaffects an electronic sensor at a sample retaining region, such as amicrowell, or that indirectly affects such an electronic sensor by abyproduct from a reaction involving such molecule or biological celllocated in such a sample retaining region, or reaction confinementregion, such as a microwell. In one aspect, analyte is a nucleic acidtemplate that is subjected to a sequencing reaction which, in turn,generates a reaction byproduct, such as hydrogen ions, that affects anelectronic sensor. The term “analyte” also comprehends multiple copiesof analytes, such as proteins, peptide, nucleic acids, or the like,attached to solid supports, such as beads or particles. In a oneembodiment, the term “analyte” means a nucleic acid amplicon or a solidphase amplicon.

“Microfluidics device” means an integrated system of one or morechambers, ports, and channels that are interconnected and in fluidcommunication and designed for carrying out an analytical reaction orprocess, either alone or in cooperation with an appliance or instrumentthat provides support functions, such as sample introduction, fluidand/or reagent driving means, temperature control, detection systems,data collection and/or integration systems, and the like. Microfluidicsdevices may further include valves, pumps, and specialized functionalcoatings on interior walls to, for example. prevent adsorption of samplecomponents or reactants, facilitate reagent movement by electroosmosis,or the like. Such devices are usually fabricated in or as a solidsubstrate, which may be glass, plastic, or other solid polymericmaterials, and typically have a planar format for case of detecting andmonitoring sample and reagent movement, especially via optical orelectrochemical methods. Features of a microfluidic device usually havecross-sectional dimensions of less than a few hundred square micrometersand passages typically have capillary dimensions, e.g. having maximalcross-sectional dimensions of from about 0.1 μm to about 500 μm.Microfluidics devices typically have volume capacities in the range offrom a few nL, e.g. 10-100 nL to 1 μL. The fabrication and operation ofmicrofluidics devices are well-known in the art as exemplified by thefollowing references that are incorporated by reference: Ramsey, U.S.Pat. Nos. 6,001,229, 5,858,195, 6,010,607, and 6,033,546; Soane et al.,U.S. Pat. Nos. 5,126,022 and 6,054,034; Nelson et al., U.S. Pat. No.6,613,525; Maher et al., U.S. Pat. No. 6,399,952; Ricco et al.,International patent publication WO 02/24322; Bjornson et al.,International patent publication WO 99/19717; Wilding et al., U.S. Pat.Nos. 5,587,128; 5,498,392; Sia et al., Electrophoresis, 24: 3563-3576(2003); Unger et al., Science, 288: 113-116 (2000); Enzelberger et al.,U.S. Pat. No. 6,960,437.

“Microwell,” which is used interchangeably with “reaction chamber,”means a special case of a “reaction confinement region,” that is, aphysical or chemical attribute of a solid substrate that permit thelocalization of a reaction of interest. Reaction confinement regions maybe a discrete region of a surface of a substrate that specifically bindsan analyte of interest, such as a discrete region with oligonucleotidesor antibodies covalently linked to such surface. Usually reactionconfinement regions are hollows or wells having well-defined shapes andvolumes which are manufactured into a substrate. These latter types ofreaction confinement regions are referred to herein as microwells orreaction chambers, and may be fabricated using conventionalmicrofabrication techniques, for example, as disclosed in the followingreferences: Doering and Nishi, Editors, Handbook of SemiconductorManufacturing Technology, Second Edition (CRC Press, 2007); Saliterman,Fundamentals of BioMEMS and Medical Microdevices (SPIE Publications,2006); Elwenspoek et al., Silicon Micromachining (Cambridge UniversityPress, 2004); and the like. Configurations (e.g., spacing, shape andvolumes) of microwells or reaction chambers are disclosed in Rothberg etal., U.S. patent publication 2009/0127589; Rothberg et al., U.K. patentapplication GB24611127, which are incorporated by reference. Microwellsmay have square, rectangular, or octagonal cross sections and bearranged as a rectilinear array on a surface. Microwells may also havehexagonal cross sections and be arranged as a hexagonal array, whichpermit a higher density of microwells per unit area in comparison torectilinear arrays. Exemplary configurations of microwells have 10²,10³, 10⁴, 10⁵, 10⁶ or 10⁷ reaction chambers.

As used herein, an “array” is a planar arrangement of elements such assensors or wells. The array may be one or two dimensional. A onedimensional array is an array having one column (or row) of elements inthe first dimension and a plurality of columns (or rows) in the seconddimension. The number of columns (or rows) in the first and seconddimensions may or may not be the same. The array may include, forexample, at least 100,000 chambers. Further, each reaction chamber has ahorizontal width and a vertical depth with, for example, an aspect ratioof about 1:1 or less. The pitch between the reaction chambers is no morethan about 10 microns, for example. Briefly, in one embodiment,microwell arrays may be fabricated after the semiconductor structures ofa sensor array are formed, in which the microwell structure is appliedto such structure on the semiconductor die. That is, the microwellstructure can be formed on the die or it may be formed separately andthen mounted onto the die.

To form the microwell structure on the die, various fabricationprocesses may be used. For example, the entire die may be spin-coatedwith, for example, a negative photoresist such as Microchem's SU-8 2015or a positive resist/polyimide such as HD Microsystems HD8820, to thedesired height of the microwells. The desired height of the wells (e.g.,about 3-12 μm in the example of one pixel per well, though not solimited as a general matter) in the photoresist layer(s) can be achievedby spinning the appropriate resist at predetermined rates (which can befound by reference to the literature and manufacturer specifications, orempirically), in one or more layers. (Well height typically may beselected in correspondence with the lateral dimension of the sensorpixel for a nominal 1:1-1.5:1 aspect ratio, height:width or diameter.)Alternatively, multiple layers of different photoresists may be appliedor another form of dielectric material may be deposited. Various typesof chemical vapor deposition may also be used to build up a layer ofmaterials suitable for microwell formation therein. In one embodiment,microwells are formed in a layer of tetra-methyl-ortho-silicate (TEOS).The invention encompasses an apparatus comprising at least onetwo-dimensional array of reaction chambers, wherein each reactionchamber is coupled to a chemically-sensitive field effect transistor(“chemFET”) and each reaction chamber is no greater than 10³ μm³ (i.e.,1 pL) in volume. Each reaction chamber is no greater than 0.34 pL, andno greater than 0.096 pL or even 0.012 pL in volume. A reaction chambercan optionally be 0.5², 1, 2², 3², 4², 5², 6², 7², 8², 9², or 10² squaremicrons in cross-sectional area at the top. The array can have at least10², 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, or more reaction chambers. Thereaction chambers may be capacitively coupled to the chemFETs.

“Primer” means an oligonucleotide, either natural or synthetic that iscapable, upon forming a duplex with a polynucleotide template, of actingas a point of initiation of nucleic acid synthesis and being extendedfrom its 3′ end along the template so that an extended duplex is formed.Extension of a primer is usually carried out with a nucleic acidpolymerase, such as a DNA or RNA polymerase. The sequence of nucleotidesadded in the extension process is determined by the sequence of thetemplate polynucleotide. Usually primers are extended by a DNApolymerase. Primers usually have a length in the range of from 14 to 40nucleotides, or in the range of from 18 to 36 nucleotides. Primers areemployed in a variety of nucleic amplification reactions, for example,linear amplification reactions using a single primer, or polymerasechain reactions, employing two or more primers. Guidance for selectingthe lengths and sequences of primers for particular applications is wellknown to those of ordinary skill in the art, as evidenced by thefollowing references that are incorporated by reference: Dieffenbach,editor, PCR Primer: A Laboratory Manual, 2nd Edition (Cold Spring HarborPress, New York, 2003).

What is claimed is:
 1. A device comprising: a substrate providing anarray of chemical sensitive sensors, a sensor of the array of chemicalsensitive sensors including a sensor pad; a well structure defining anarray of wells disposed over the array of chemical sensitive sensors, awell of the array of wells corresponding with the sensor pad of thesensor of the array of chemical sensitive sensors, the well structuredefining a sidewall of the well, a bottom of the well disposed over thesensor pad; and a chemical disposed over the sensor pad, the chemicalincluding a functional group selected from the group consisting ofphosphate, phosphonate, catechol, nitrocatechol, boronate,phenylboronate, imidazole, and silanol.
 2. The device of claim 1,wherein the sidewall of the well is substantially free of the chemical.3. The device of claim 1, wherein the functional group is selected fromthe group consisting of phosphate, phosphonate, catechol, andnitrocatechol.
 4. The device of claim 3, wherein the functional group isselected from the group consisting of phosphate and phosphonate.
 5. Thedevice of claim 1, wherein the functional group includes phosphonate. 6.The device of claim 1, wherein the chemical sensitive sensors are fieldeffect transistor sensors.
 7. The device of claim 1, the substrateincludes a CMOS layer and the chemical sensitive sensors are CMOSdevices.
 8. The device of claim 1, further comprising a silane chemicaldisposed on the sidewall and not the bottom of the well of the array ofwells, the silane chemical having the formula R—[Yn]—Si—[X1X2X3],wherein R is an organofunctional group, Y is (CH2) or (C2H4O), n is aninteger, and [X1X2X3] comprises one or more hydrolysable groups.
 9. Thedevice of claim 8, wherein [X1X2X3] includes an alkoxy group.
 10. Thedevice of claim 9, wherein the silane chemical is a trialkoxy silanechemical.
 11. The device of claim 9, wherein the silane chemical is adialkoxy silane chemical.
 12. The device of claim 8, wherein [X1X2X3]includes a halogen group.
 13. The device of claim 8, wherein Y is (CH2)and n is an integer from 1 to
 20. 14. The device of claim 8, wherein Yis (C2H4O) and n is an integer from 1 to
 100. 15. The device of claim 8,wherein R is selected from the group consisting of methyl, methylene,phenyl, benzyl, anilino, amino, amide, hydroxyl, aldehyde, alkoxy, halo,mercapto, carboxy, acyl, vinyl, allyl, styryl, epoxy, isocyanato,glycidoxy, and acryloxy.
 16. The device of claim 8, wherein R is anamino group.
 17. The device of claim 8, wherein R is an amide group. 18.The device of claim 1, wherein the well structure comprises an oxide ofsilicon.
 19. The device of claim 1, wherein an exposed portion of thesensor pad includes a metal oxide.
 20. The device of claim 1, furthercomprising a metal oxide disposed over the sensor pad, the metal oxideselected from the group consisting of tantalum oxide, hafnium oxide,zirconium oxide, and aluminum oxide.